Sodium in PDB 8pz0: Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.

Enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.

All present enzymatic activity of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14., PDB code: 8pz0 was solved by M.C.Simpson, C.M.Czekster, C.J.Harding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.49 / 1.80
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 181.95, 181.95, 87.43, 90, 90, 120
R / Rfree (%) 16.8 / 19

Other elements in 8pz0:

The structure of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. (pdb code 8pz0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14., PDB code: 8pz0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8pz0

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Sodium binding site 1 out of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:32.6
occ:1.00
 OD2 A:ASP310 1.8 50.2 1.0
O A:HOH749 2.1 53.9 1.0
OE2 A:GLU371 2.1 47.0 1.0
NZ A:LYS287 2.3 53.8 1.0
OD2 A:ASP292 2.5 42.0 1.0
CG A:ASP310 2.7 56.9 1.0
OD1 A:ASP310 3.1 48.0 1.0
CD A:GLU371 3.1 42.3 1.0
NA A:NA610 3.2 40.8 1.0
CE A:LYS287 3.2 42.7 1.0
CG A:ASP292 3.3 46.3 1.0
OE1 A:GLU371 3.5 49.0 1.0
O2 A:BCT605 3.7 53.7 1.0
CB A:ASP292 3.8 42.2 1.0
CB A:ASP310 4.1 40.2 1.0
OD1 A:ASP292 4.3 42.4 1.0
O A:THR396 4.3 38.9 1.0
CG A:GLU371 4.5 43.2 1.0
CG2 A:ILE289 4.5 37.2 1.0
CB A:ILE289 4.5 34.8 1.0
CG1 A:ILE289 4.6 38.1 1.0
CD A:LYS287 4.6 37.9 1.0
N A:GLY372 4.6 41.0 1.0
O A:ASP369 4.8 41.4 1.0
C A:BCT605 4.9 54.5 1.0
CA A:GLY372 4.9 44.1 1.0

Sodium binding site 2 out of 5 in 8pz0

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Sodium binding site 2 out of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:63.0
occ:1.00
 N A:GLU102 2.9 54.9 1.0
O A:ALA99 2.9 44.1 1.0
CB A:GLU102 3.2 60.7 1.0
N A:LYS101 3.3 47.6 1.0
CD2 A:LEU105 3.3 50.3 1.0
C A:GLY100 3.4 47.3 1.0
CA A:GLU102 3.5 62.4 1.0
CA A:GLY100 3.5 43.0 1.0
O A:HOH994 3.6 55.7 1.0
O A:GLU102 3.7 61.1 1.0
CG A:GLU102 3.7 66.5 1.0
C A:ALA99 3.9 43.0 1.0
C A:LYS101 3.9 58.0 1.0
C A:GLU102 4.0 64.9 1.0
NE2 A:GLN109 4.1 66.2 1.0
O A:GLY100 4.1 49.2 1.0
CA A:LYS101 4.2 57.5 1.0
N A:GLY100 4.2 41.7 1.0
CG2 A:VAL77 4.5 42.6 1.0
CG A:LEU105 4.6 46.8 1.0
O A:GLU104 4.7 50.0 1.0
CD A:GLN109 4.7 60.6 1.0
OE1 A:GLN109 4.8 58.1 1.0
NH2 A:ARG47 4.9 64.8 1.0
CD A:GLU102 4.9 74.6 1.0
O A:LYS101 5.0 59.8 1.0

Sodium binding site 3 out of 5 in 8pz0

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Sodium binding site 3 out of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:63.4
occ:1.00
 CG A:GLN109 2.9 44.1 1.0
N A:GLN109 3.0 38.5 1.0
OE1 A:GLN109 3.1 58.1 1.0
CA A:GLY106 3.2 44.9 1.0
CD A:GLN109 3.3 60.6 1.0
C A:GLY106 3.4 47.9 1.0
N A:GLY106 3.4 42.0 1.0
O A:HOH939 3.4 60.8 1.0
CB A:GLN109 3.4 39.8 1.0
O A:GLY106 3.5 42.3 1.0
N A:ARG108 3.7 38.9 1.0
CA A:GLN109 3.8 39.5 1.0
CB A:ARG108 3.8 43.0 1.0
C A:ARG108 3.9 39.8 1.0
CA A:ARG108 4.0 44.0 1.0
N A:ASP107 4.1 43.4 1.0
NE2 A:GLN109 4.5 66.2 1.0
C A:ASP107 4.5 44.5 1.0
C A:LEU105 4.7 45.4 1.0
CA A:ASP107 4.9 45.0 1.0

Sodium binding site 4 out of 5 in 8pz0

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Sodium binding site 4 out of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na609

b:57.7
occ:1.00
 CA A:GLY459 2.7 55.1 1.0
OE1 A:GLN446 2.8 50.0 1.0
C A:GLY459 3.0 45.4 1.0
N A:LYS461 3.0 44.2 1.0
N A:GLY459 3.1 59.4 1.0
N A:PRO460 3.2 43.8 1.0
CD A:PRO460 3.4 50.7 1.0
CB A:LYS461 3.5 42.1 1.0
CG A:LYS461 3.6 47.1 1.0
CA A:LYS461 3.7 44.1 1.0
O A:GLY459 3.7 46.0 1.0
O A:LYS461 3.8 39.6 1.0
CD A:GLN446 3.8 51.4 1.0
C A:PRO460 4.0 45.2 1.0
CA A:PRO460 4.2 46.6 1.0
C A:LYS461 4.2 40.1 1.0
CD A:LYS461 4.3 46.3 1.0
O A:HOH753 4.3 41.4 1.0
CG A:PRO460 4.4 52.8 1.0
C A:GLY458 4.4 55.4 1.0
NE2 A:GLN446 4.4 52.0 1.0
CG A:GLN446 4.8 45.5 1.0

Sodium binding site 5 out of 5 in 8pz0

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Sodium binding site 5 out of 5 in the Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Intracellular Leucine Aminopeptidase of Pseudomonas Aeruginosa PA14. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na610

b:40.8
occ:1.00
 OD1 A:ASP369 2.1 45.2 1.0
OD2 A:ASP292 2.1 42.0 1.0
O A:ASP369 2.1 41.4 1.0
OE1 A:GLU371 2.2 49.0 1.0
O A:HOH749 2.2 53.9 1.0
CG A:ASP292 3.0 46.3 1.0
C A:ASP369 3.0 42.1 1.0
CG A:ASP369 3.1 47.3 1.0
CD A:GLU371 3.1 42.3 1.0
NA A:NA606 3.2 32.6 1.0
OD1 A:ASP292 3.3 42.4 1.0
OE2 A:GLU371 3.4 47.0 1.0
CA A:ASP369 3.5 40.9 1.0
NZ A:LYS299 3.8 47.4 1.0
CB A:ASP369 3.9 41.5 1.0
O2 A:BCT605 3.9 53.7 1.0
OD2 A:ASP369 4.0 49.0 1.0
CE A:LYS299 4.1 44.3 1.0
N A:ALA370 4.2 38.2 1.0
N A:GLU371 4.3 40.6 1.0
CB A:ASP292 4.4 42.2 1.0
CG A:GLU371 4.5 43.2 1.0
OD2 A:ASP310 4.6 50.2 1.0
CA A:ALA370 4.6 40.3 1.0
C A:BCT605 4.7 54.5 1.0
ND2 A:ASN342 4.7 41.0 1.0
CA A:GLY294 4.8 41.5 1.0
N A:ASP369 4.9 38.1 1.0
CB A:GLU371 4.9 44.0 1.0

Reference:

M.C.Simpson, C.J.Harding, R.M.Czekster, L.Remmel, B.E.Bode, C.M.Czekster. Unveiling the Catalytic Mechanism of A Processive Metalloaminopeptidase. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37924287
DOI: 10.1021/ACS.BIOCHEM.3C00420
Page generated: Wed Oct 9 13:05:13 2024

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